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Record Information
Version4.0
StatusExpected but not Quantified
Creation Date2013-06-15 18:25:05 UTC
Update Date2017-12-20 20:30:53 UTC
HMDB IDHMDB0060639
Secondary Accession Numbers
  • HMDB60639
Metabolite Identification
Common NameGemcitabine diphosphate
DescriptionGemcitabine diphosphate is a member of the class of compounds known as organic pyrophosphates. Organic pyrophosphates are organic compounds containing the pyrophosphate oxoanion, with the structure OP([O-])(=O)OP(O)([O-])=O. Gemcitabine diphosphate is soluble (in water) and a moderately acidic compound (based on its pKa). Gemcitabine diphosphate can be found primarily in blood and urine, as well as in human kidney and liver tissues. Within the cell, gemcitabine diphosphate is primarily located in the cytoplasm. In humans, gemcitabine diphosphate is involved in a couple of metabolic pathways, which include gemcitabine metabolism pathway and gemcitabine pathway. Gemcitabine diphosphate is a metabolite of gemcitabine. Gemcitabine is a nucleoside analog used as chemotherapy. It is marketed as Gemzar by Eli Lilly and Company (Wikipedia).
Structure
Thumb
SynonymsNot Available
Chemical FormulaC9H13F2N3O10P2
Average Molecular Weight423.158
Monoisotopic Molecular Weight423.004423085
IUPAC Name[({[(2R,3R,5R)-5-(4-amino-2-oxo-1,2-dihydropyrimidin-1-yl)-4,4-difluoro-3-hydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy]phosphonic acid
Traditional Name{[(2R,3R,5R)-5-(4-amino-2-oxopyrimidin-1-yl)-4,4-difluoro-3-hydroxyoxolan-2-yl]methoxy(hydroxy)phosphoryl}oxyphosphonic acid
CAS Registry NumberNot Available
SMILES
NC1=NC(=O)N(C=C1)[C@@H]1O[C@H](COP(O)(=O)OP(O)(O)=O)[C@@H](O)C1(F)F
InChI Identifier
InChI=1S/C9H13F2N3O10P2/c10-9(11)6(15)4(3-22-26(20,21)24-25(17,18)19)23-7(9)14-2-1-5(12)13-8(14)16/h1-2,4,6-7,15H,3H2,(H,20,21)(H2,12,13,16)(H2,17,18,19)/t4-,6-,7-/m1/s1
InChI KeyFRQISCZGNNXEMD-QPPQHZFASA-N
Chemical Taxonomy
DescriptionThis compound belongs to the class of organic compounds known as organic pyrophosphates. These are organic compounds containing the pyrophosphate oxoanion, with the structure OP([O-])(=O)OP(O)([O-])=O.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganic oxoanionic compounds
Sub ClassOrganic pyrophosphates
Direct ParentOrganic pyrophosphates
Alternative Parents
Substituents
  • Organic pyrophosphate
  • Aminopyrimidine
  • Monoalkyl phosphate
  • Pyrimidone
  • Hydropyrimidine
  • Organic phosphoric acid derivative
  • Phosphoric acid ester
  • Imidolactam
  • Alkyl phosphate
  • Pyrimidine
  • Heteroaromatic compound
  • Tetrahydrofuran
  • Fluorohydrin
  • Halohydrin
  • Secondary alcohol
  • Oxacycle
  • Azacycle
  • Organoheterocyclic compound
  • Organonitrogen compound
  • Organofluoride
  • Alkyl fluoride
  • Alcohol
  • Organohalogen compound
  • Hydrocarbon derivative
  • Organic oxide
  • Organopnictogen compound
  • Organic nitrogen compound
  • Amine
  • Organooxygen compound
  • Alkyl halide
  • Primary amine
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External DescriptorsNot Available
Ontology
Disposition

Source:

Biological location:

Process

Naturally occurring process:

Role

Biological role:

Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
Water Solubility14.1 g/LALOGPS
logP-0.13ALOGPS
logP-2ChemAxon
logS-1.5ALOGPS
pKa (Strongest Acidic)1.77ChemAxon
pKa (Strongest Basic)-0.68ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count10ChemAxon
Hydrogen Donor Count5ChemAxon
Polar Surface Area201.44 ŲChemAxon
Rotatable Bond Count6ChemAxon
Refractivity75 m³·mol⁻¹ChemAxon
Polarizability30.87 ųChemAxon
Number of Rings2ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectra
Spectrum TypeDescriptionSplash Key
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-004i-9822000000-398b68b48bd8b607ab48View in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positivesplash10-004j-7902100000-9dee865b2e3781388e98View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-03di-0900000000-3d1c9663915e837da690View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03di-3900000000-dd3bbc564bd91568165cView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-03xs-9500000000-cee67b52b763745a6147View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-03fr-1902200000-5af728a0ab758e0c9066View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-01t9-9400000000-866bffe8f7fa8b19fb0bView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-ea4cfe6db1a21d040c1cView in MoNA
Biological Properties
Cellular Locations
  • Cytoplasm
Biospecimen Locations
  • Blood
  • Urine
Tissue Location
  • Kidney
  • Liver
Pathways
NameSMPDB/PathwhizKEGG
Gemcitabine Action PathwayThumbThumb?image type=greyscaleThumb?image type=simpleNot Available
Gemcitabine Metabolism PathwayThumbThumb?image type=greyscaleThumb?image type=simpleNot Available
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodExpected but not Quantified Not AvailableNot AvailableNormal
    details
    UrineExpected but not Quantified Not AvailableNot AvailableNormal
      details
      Abnormal Concentrations
      Not Available
      Associated Disorders and Diseases
      Disease ReferencesNone
      Associated OMIM IDsNone
      DrugBank IDNot Available
      Phenol Explorer Compound IDNot Available
      FoodDB IDNot Available
      KNApSAcK IDNot Available
      Chemspider IDNot Available
      KEGG Compound IDNot Available
      BioCyc IDNot Available
      BiGG IDNot Available
      Wikipedia LinkNot Available
      METLIN IDNot Available
      PubChem Compound6420157
      PDB IDGCQ
      ChEBI IDNot Available
      References
      Synthesis ReferenceNot Available
      Material Safety Data Sheet (MSDS)Not Available
      General ReferencesNot Available